Phylogeography reveals routes of colonization of the bark beetle Dendroctonus approximatus Dietz in Mexico

Rearranging and completing the puzzle: Phylogenomic analysis of bark beetles Dendroctonus reveals new hypotheses about genus diversification

Studies carried out on bark beetles within Dendroctonus have been extensive and revealed diverse information in different areas of their natural history, taxonomy, evolution, and interactions, among others. Despite these efforts, phylogenetic hypotheses have remained obscured mainly due to limited information analyzed (taxonomic, gene sampling, or both) in studies focused on obtaining evolutionary hypotheses for this genus. With the aim of filling these gaps in the evolutionary history for Dendroctonus, we analyzed ∼1800 loci mapped to a reference genome obtained for 20 of the 21 species recognized to date, minimizing the impact of missing information and improving the assumption of orthology in a phylogenomic framework. We obtained congruent phylogenetic topologies from two phylogenomic inference strategies: loci concatenation (ML framework) and a multispecies coalescent model (MSC) through the analysis of site pattern frequencies (SNPs). Dendroctonus is composed of two major clades (A and B), each containing five and four subclades, respectively. According to our divergence dating analysis, the MRCA for Dendroctonus dates back to the early Eocene, while the MRCA for each major clade diverged in the mid-Eocene. Interestingly, most of the speciation events of extant species occurred during the Miocene, which could be correlated with the diversification of pine trees (Pinus). The MRCA for Dendroctonus inhabited large regions of North America, with all ancestors and descendants of clade A having diversified within this region. The Mexican Transition Zone is important in the diversification processes for the majority of clade A species. For clade B, we identified two important colonization events to the Old World from America: the first in the early Oligocene from the Arctic to Asia (via Beringia), and the second during the Miocene from the Arctic-Western-Alleghany region to Europe and Siberia (also via Beringia). Our genomic analyses also supported the existence of hidden structured lineages within the frontalis complex, and also that D. beckeri represent a lineage independent from D. valens, as previously suggested. The information presented here updates the knowledge concerning the diversification of a genus with remarkable ecological and economic importance.

Phylogeography of Falagonia mexicana Sharp, 1883 (Coleoptera, Staphylinidae, Aleocharinae)

Falagonia mexicana is an aleocharine distributed from northern Mexico to Guatemala and El Salvador. It is associated with Atta mexicana ants and lives within their piles of waste or external debris. The phylogeography and historical demography of 18 populations from Mexico, Guatemala, and El Salvador were studied. The data set encompasses a 472 bp fragment of the COI. Results suggest that F. mexicana was originated during Middle Pliocene (ca. 0.5 Mya), starting its diversification at the Upper Pleistocene and Holocene. Populations were recovered forming at least four main lineages, with a significant phylogeographic structure. Evidence of contemporary restricted gene flow was found among populations. The historical demography suggests that the geographic structure is due to recent physical barriers (e.g., Isthmus of Tehuantepec) rather than ancient geological events. Also, recent geological and volcanic events in the east of the Trans-Mexican Volcanic Belt and the Sierra Madre Oriental might be responsible for the restricted gene flow among populations. Skyline-plot analyses suggested that a demographic expansion event took place at the end of the Late Quaternary glacial-interglacial cycles.

Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae)

PREMISE OF THE STUDY

Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation, thereby becoming separated by topography.

METHODS

We inferred orthologs from transcriptomes of five species and sequenced these in 42 individuals representing all Dioon species. From these data and published plastid sequences, we inferred dated species trees and lineage-specific diversification rates.

KEY RESULTS

Analyses of 84 newly sequenced nuclear orthologs and published plastid data confirm four major clades within Dioon, all of Pleistocene age. Gene tree analysis, divergence dates, and an increase in diversification rate support very recent and rapid divergence of extant taxa.

CONCLUSIONS

This study confirms the Pleistocene age of Dioon species and implicates Pleistocene climate change and established topography in lineage spitting. These results add to our understanding of the cycads as evolutionarily dynamic lineages, not relicts or evolutionary dead ends. We also find that well-supported secondary calibration points can be reliable in the absence of fossils. Our hypothesis of lineage splitting mediated by habitat shifts may be applicable to other taxa that are restricted to elevation specific ecotones.

Phylogeography of specialist weevil Trichobaris soror: a seed predator of Datura stramonium

Can the genetic structure of a specialist weevil be explained by the geological history of their distribution zone? We analyze the genetic variation of the weevil Trichobaris soror, a specialist seed predator of Datura stramonium, in order to address this question. For the phylogeographic analysis we used the COI gene, and assessed species identity in weevil populations through geometric morphometric approach. In total, we found 53 haplotypes in 413 samples, whose genetic variation supports the formation of three groups: (1) the Transmexican Volcanic Belt (TVB group), (2) the Sierra Madre Sur (SMS group) and (3) the Balsas Basin (BB group). The morphometric analysis suggests that BB group is probably not T. soror. Our results have two implications: first, the phylogeographic pattern of T. soror is explained by both the formation of the geological provinces where it is currently distributed and the coevolution with its host plant, because the TVB and SMS groups could be separated due to the discontinuity of altitude between the geological provinces, but the recent population expansion of TVB group and the high frequency of only one haplotype can be due to specialization to the host plant. Second, we report a new record of a different species of weevil in BB group parasitizing D. stramonium fruits.